Star Trek The Mass Effect
by HeirOfRohan
Summary: After the Khan Incident, the USS Enterprise continues her five-year long mission of discovery and exploration. What started out as a routine scanning mission of an unmapped star system triggers a chain of events that would shake the very foundations of the galaxy. With new races, new cultures, and a new enemy that was as old as the galaxy itself — the Reapers.


**_Foreword:_** _I do not own Mass Effect or Star Trek. They belong to both Bioware and Gene Rodenberry respectively._

* * *

 ** _Star Trek: The Mass Effect_**

* * *

 _"_ _Space: the final frontier. These are the voyages of the starship_ Enterprise _. Her continuing mission: to explore strange new worlds, to seek out new life forms and new civilizations, to boldly go where no one has gone before."_

 _–_ _Spock Prime, Ambassador of New Vulcan, stardate 2258_

* * *

 ** _Prologue_**

* * *

Space.

An endless expanse of vast possibilities and source of intrigue for many centuries, for countless generations many civilizations once looked up towards the stars, wondering about the possibilities that lay far beyond the inky blackness of illuminated vacuum. For many of them, they found new worlds, new species and new avenues for a peaceful and a comfortable existence in which the worries of any mortal could be laid aside, and enjoy their lives.

But that was mere wishful thinking, as ancient scholars once said,

 _'_ _The infinite unknown holds the most dangerous of secrets.'_

Many of their society just waved off their concerns, labelling them as paranoid or in some cases 'disillusioned madmen'. And thousands of years later, society would have to eat their words … if they lived long enough to realize their folly.

That was the reality many spacefaring civilizations eons past had faced, and each one of them payed for their naiveté with their brutal extinction. Countless trillions were lost in a never ending cycle of death and destruction that spanned the Milky Way galaxy for over two billion years, their will crushed and worlds burned to ashes, with each rise of advanced civilizations heralded their untimely end fifty thousand years later, and the cycle repeats once more. Many tried to fight back, albeit futilely, as they were no match for the calamity that consumed them like how matter was absorbed into a black hole.

But, through this bleak and dark past rises a beacon of hope, as after thousands of cycles, the wheels of fate had begun to turn, and the cycle shall finally come to an end …

* * *

 ** _Location: Exodus Cluster / Utopia System / Eden Prime / Timestamp – 52,258 BC_**

Raul'Dan looked onwards through the viewscreen of his modified heavy cruiser as he watched helplessly as his homeworld, the garden world colony of Eden Prime, was burned to the ground, as noted by the orange illuminations of flames and brief flashes of light from the surface and in orbit around the doomed planet. He closed his four slitted eyes in mourning, his carapace-covered head bowed low, as he knew there was nothing that he could do that could even remotely help his people on the planet below. It made him all the more determined to stop the ones responsible for his species imminent extinction:

The Reapers.

Hulking, onyx technological monstrosities of unfathomable power and destructive capability that possessed technology that far surpassed everything they ever owned or created, as the black ships' mastery over the revolutionary Mass Effect technology that Raul's civilization had solely depended upon for the past five thousand years would make their most innovative achievements look like child's play. And the Reapers know it, and these synthetic harbingers of death capitalized on that fact with _brutal_ efficiency.

In fact, now that Raul had time to think about it in detail, it was as if the technologies that they had discovered five millennia ago, the fabled Mass Relays and the Citadel – a massive space station and center of their interstellar empire – were created by these synthetics specifically for them to find and harness them, and it worked like a charm as the Mass Relays catapulted their technological level by two hundred years.

Raul narrowed his eyes as his suspicions about the Mass Relays were correct: the greatest discovery of his race was in fact their greatest mistake … as they had unwillingly been caught in a trap that was placed in motion eons in the making.

For years Raul had been studying these ancient conduits, tuning fork-shaped structures powered by an immensely powerful Element Zero Core that can propel any starship from one system to another in which another Mass Relay was there as a receiver, in less than a minute. The concept of faster-than-light travel could not have been possible without them, but Raul's suspicions were raised to their peak when he made a startling discovery, just before his escort fleet had been ambushed by the black ships two years ago.

Raul had stumbled upon a command in the Mass Relays' programming which stated that when a certain command or code was issued, it would shut down nearly _all_ of the relays located throughout the inner core worlds of the Milky Way galaxy, rendering FTL travel hopeless, and the Reapers have no trouble reactivating the relays to jump though … as they were ones who gave the order.

But unfortunately for Raul and his race, they learned about that particular fact too little too late …

Raul'Dan sighed as he gazed at the battered fleet that had been vainly trying to mount an effective defense against the Reapers, but crimson lances of death heralded by breached hulls and decompressing bulkheads followed by massive explosions as the ships' mass effect core overloaded from the sheer overwhelming firepower of the Reapers. This hopeless sight, of his people futilely fighting against an enemy that knew everything there was to be known about Mass Effect, literally turning their own technology against them, was what finally drove Raul to his decision.

No civilization could survive while being dependent on Mass Effect technology, not while the Reapers were still out there. Having had the final preparations completed, it was only a matter of time before they have to depart as their stealth systems couldn't fool the Reaper's advanced sensors for long.

Hearing a door hiss open to his side, Raul glanced at the newcomer who saluted him smartly, decked out in full body armor and a pressurized suit. Raul inclined his head in greeting, "What brings you here, Centurion Can'Deoth?"

The newly named Can'Deoth nodded. "All preparations are complete Avatar," he announced, "Admiral Caeo'Dan has sent me here to inform you that you are needed on the bridge in haste."

"Ah yes, Caeo." Raul nodded with grim expression. "I'll head over there right away." He watched as Can'Deoth saluted once more before pivoting and headed on his way, with Raul himself following soon after his wake.

Walking past the crew quarters on Deck Two, he saw dozens of scientists and engineers going over data and reports from the frontline that may suggest a way to defeating their adversary, and by the looks on their faces, they were very bad news.

Forcing himself to not think about the lives that were lost, Raul made haste towards the elevator which took him up to the Combat Information Center, where a lone male stood on the command pedestal eyes glued forward on the holographic screen as he watched the terrible events unfold. Other people were working on their consoles keeping the pride of the fleet running as Raul stepped off the elevator.

The other male must have heard Raul's arrival as he turned to meet him, his carapace a slightly darker shade of brown with similar slitted yellow eyes stared at Raul with respect and weariness. The male saluted him as Raul stood in front of him, making him wave his hand off in dismissal.

"Save the formal greeting Admiral, there's a time and place for that," Raul said with an admonishing tone, causing the other male to frown slightly, before Raul's eyes softened. "It's good to see you little brother."

The newly named Admiral Caeo'Dan smiled as he shook Raul's hand. "Likewise big brother."

"How's the situation planetside?" he knew it was a foolish question to ask, but he didn't become his people's Avatar of Peace for callously wasting the lives of his subordinates.

The Admiral shook his head gravely. "Not good. The Grand Army put up a good fight, but they were overwhelmed." He reported with a sad sigh, "Resistance planetside is dying down. Civilian populations are being liquefied and harvested as we speak. We have lost, Avatar."

"I know," Raul said with a sigh, before a determined gleam entered his eyes, "We have lost many battles, but we have not lost the war," the bridge crew turned to look at him as he spoke, their sorrowful expressions gained a bit of hope from his words. "As of right now, we, the seventy members of the elite crew of the _Cyrano,_ are one of the last members of the Prothean Empire … but take heart everyone," he said as he saw the crew members becoming depressed as he said they were the last, and he needed to fix that. "We _shall_ prevail. Not right now, but in hundreds, or maybe ten thousand years from now we will prevail, and finally let the souls of our people rest in eternal peace. The Reapers may think they have destroyed us, but we have something that they don't have: _determination_ and the will to fight on!"

The crew erupted in cheers as Raul continued to speak, "As of right now, we must avoid direct engagement with the Reapers at all costs, as we are the last of our race, and we must survive so that other cultures that come after our Empire's demise would know about the coming calamity. Forewarned is forearmed, and after the Reapers are finally defeated, we will walk on their dead hulks and desecrate them with our fury!" The crew erupted into cheers and hoots again as Raul turned to face Caeo'Dan.

"Admiral, plot a course for the Arcturus System, and hide us in the magnetic rings orbiting the second planet," Raul ordered as the bridge crew worked fervently to carry out their Avatar's orders, "The magnetic field should make us invisible to even the most advanced scanners the Reapers possessed, and we'll wait until they depart before moving out again. I'll put everyone in cryo-stasis by then."

"Yes sir." Caeo saluted before issuing orders as Raul set about to put his people into cryo sleep.

The large silhouette of the _Cyrano_ maneuvered away from the doomed planet, undetectable and silent as it moored near the massive construct of the system's Mass Relay, before a blue electrifying energy enveloped the vessel before it shot into the void, leaving a blue trail in its wake.

* * *

Raul opened his eyes as he slowly but groggily woke up from cryo sleep. His limbs were unresponsive and he took time to gather his bearings before a surge of adrenaline filtered through his blood stream, finally enabling him to feel his limbs and climb out of the cryo pod he was in.

He turned to a pedestal and spoke, "Ophis, sitrep."

A green-yellow hologram appeared on the pedestal which resembled a female Prothean spoke in a synthesized voice, _"Power level is at optimum level. All systems at seventy five percent readiness. Reaper threat level, low. Scans show that the Reapers have left known space and are proceeding towards dark space."_ The Virtual Intelligence of the _Cyrano_ reported.

Raul sighed in relief at the news. "Timestamp?"

 _"_ _Exactly thirty eight thousand six hundred and ninety six days, three hours, seven minutes and thirteen seconds has passed since entering cryo-stasis Avatar."_ The VI reported again.

Raul's eyes widened, a bitter smile of pride on his lips. The Prothean Empire held out for over a century against the blasted Reapers before finally succumbing to their might. A truly worthy footnote in the annals of galactic history — if they could preserve it.

"I see … wake the others."

 _"_ _Understood."_

It took another two hours for the entire to crew to stave off the effects of cryo-sleep and keep informed of their current situation, and their drive to defeat the Reapers burned even stronger as Raul met with the highest ranking officers on the bridge. They were the last of their race, and sitting around him, three males and two females, are all that's left of their government …

"Ladies and Gentlemen, I will be brief, since you're already been informed of my plan," Raul spoke seriously as he eyed each member of his staff, "We will go through the Arcturus Relay to the Sol System, where on the third planet orbiting the star of Sol has signs of sentient life on them since we have begun studying them years ago.

"We will jump in, and we'll destroy the Sol Relay, along with the relay hub in Arcturus with the experimental slug that my department back at Eden Prime had been developing, which overloads the eezo core of the Mass Relay, effectively imploding it without it going hypernova on us as it did on Thyferra …" the Thyferra system had once had a Mass Relay, but an interplanetary war between two pre-interstellar travel species had destroyed it, and the subsequent explosion erased the entire system off the face of the galaxy, the two waring species included.

Since then, the Prothean Military had been researching of ways to destroy or manipulate the Mass Relays without risk of blowing up entire systems, and Raul's department was working on the former project …

"I know many of you reject this plan, but it is the best way to ensure this sector of space beyond this Mass Relay could ever have a chance against the Reapers." He said with utmost conviction, "You saw what happened to our race. The Reapers used our own technology against us, and the Mass Relays are just more traps to lure more sentient beings to activate and exploit its technology, leading to their own demise as well. By destroying this Mass Relay, hopefully the sentient beings on the third planet of the star manage to advance on their own without relying on the technology that ultimately doomed us." The other Protheans looked at him gravely as he spoke the truth, "We can't throw these people onto a path they didn't choose, and repeat the mistakes we made. The Mass Relays, the Citadel … it may take millennia for the natives to advance, but they would hopefully be ready when they come back."

Raul looked down as he sighed, before looking back up at his staff, specifically his brother. "For the Glory of the Empire …" he murmured.

"For the Glory of the Empire," the rest of the staff echoed as they saluted before walking away to resumed their duties, determined to make the sacrifice of their people count.

Raul noticed that Caeo had stayed behind, as he addressed him. "Something on your mind, Admiral?"

Caeo shook his head no as he looked as his brother skeptically. "You're sure putting a lot faith with these natives … are you sure that's wise?"

Raul shook his head wearily, "Only time will tell, brother. It is a risky gamble, but we can't afford to be picky about our methods anymore, we know the Reapers wouldn't allow that …" he explained, earning a nod from the Admiral. "Our brothers on Ilos have already severed the Reaper's control over the Keepers of the Citadel, so in the next cycle, they couldn't go through the Citadel even if they wanted to."

"Well, whatever your choice is, my crew and I are always behind you, a hundred percent." Caeo saluted, "You can count on that, Avatar."

"Thank you, Admiral."

Pivoting on his heels, Caeo made his way towards the bridge to bring the _Cyrano_ out of the magnetic rings of the planet below them. The massive Prothean heavy cruiser glided out of the dusty brown rings of the planet before turning on its axis and propelled towards the Mass Relay. With a flash of blue light, the _Cyrano_ disappeared into the void, never to be seen again.

* * *

It took nearly five months, first destroying the Sol Relay and Arcturus Relay hub and removing their parts and pieces so that it couldn't be salvaged by any means, and then destroying the outpost the Protheans had constructed on the third planet to act as a research station. The crew of the _Cyrano_ left nothing standing, not even footprints as they blew up the outpost with copious amounts of explosives. After that, the _Cyrano_ proceeded to scuttle the orbiting platforms surrounding the planet and the ones on the adjacent planets were either scuttled or towed towards the star to be atomized.

And that left the base on the fourth planet of the system, a red rusty planet that was barely suitable for organic life. Even here, the research outpost was blown to bits and the _Cyrano_ itself, after a farewell ceremony, was put on a collision course with the system's star, as the scientists deemed the _Cyrano_ to be too advanced in Mass Effect technology to be left with their care.

The only things left of their existence in this system was the underground bunker that also served as a last resort command center in the event the Prothean Empire collapsed. Bringing with the seventy or so crewmen were supplies and ample amounts of power cells to power the cryogenic pods to last them for a long, long time.

The crew was already in the process of entering cryo-sleep as Raul held a last minute meeting with his staff before going into cryo-sleep himself. Their next meeting would be when the natives on the third planet had discovered the Mass Relay either at the Arcturus System or the Exodus Cluster, in which the VI, Ophis, would wake them from cryo.

The six Protheans were the last ones to enter their pods as they checked the sixty-five survivors of their race and finding them to be stable. They then entered their pods one by one until it only left Raul and Caeo left, who were both doing last minute checks in the command center before shutting the base's power excluding the cryo pods and life support.

The underground base was nigh undetectable by normal means, and only someone or something small are brave enough to go down a deep, several mile high chasm to search for the bunker.

Raul sighed as he sat in his command chair. "And so the wait begins."

Caeo nodded. "Let's hope the natives do what you envisioned them to do."

"So do I, brother …" Raul murmured as he rubbed his eyes, "So do I." he said before ordering Ophis to redirect solar power to power the cryo pods to extend their functionality by another ten years.

Caeo was the first into his pod, letting the top close down on him before closing his eyes and slept.

Raul paused as he had one foot into his pod already, before glancing up at the ceiling of the bunker, silently praying that his intentions were not in vain, before heading into cryo-sleep as well.

Little did he know that his decision of destroying the Mass Relay would have far reaching consequences, and it will change the fates of not just the natives, but the fate of the entire Milky Way galaxy as they all know it. If only Raul'Dan, Avatar of Peace for the Prothean Race, could fathom just how one simple choice of sparing one species the fate which consumes all races, would finally end a two billion year old cycle of genocide …

* * *

 **And. We. Are. Done!**

 **Wassup guys!? This is my first attempt at a crossover with one of my favorite movies and one of my favorite games. So please, rate and review my story, as always! And be warned though ... the United Federation of Planets is going to be a force to be reckoned with in the Mass Effect Universe! Because, hint, hint, phasers against kinetic barriers, who would win? You decide!**

 **This is HEIROFROHAN signing off,**

 **PEACE!**


End file.
